Circulating Tumor DNA Dynamics Predict Response to Neoadjuvant Chemotherapy in PIK3CA-Mutated...

Background: The clinical significance of circulating tumor DNA (ctDNA) dynamics in PIK3CA-mutated breast cancer treated with neoadjuvant chemotherapy (NAC) remains unclear. We evaluated whether ctDNA patterns defined between baseline and pre-surgery are associated with pathological complete response (pCR) and long-term distant outcomes. Methods: A total of 122 patients with stage I-III breast cancer who were scheduled to receive NAC between May 2016 and September 2017 were prospectively enrolled in this study. Tumor DNA extracted from pretreatment formalin-fixed, paraffin-embedded (FFPE) biopsy specimens was analyzed for PIK3CA hotspot mutations (E542K, E545K, and H1047R) using droplet digital PCR (ddPCR). Blood samples were collected at baseline (pre-NAC), pre-surgery, and post-surgery. Tumor-matched PIK3CA-mutated ctDNA was quantified by ddPCR. ctDNA dynamics between baseline and pre-surgery were categorized into four patterns: persistent-negative (-/-), cleared (+/-), persistent-positive (+/+), and post-NAC-emergent (-/+). pCR was defined as the complete disappearance of invasive carcinoma in both the breast and lymph nodes. Distant metastasis was assessed after a median follow-up of 96 months (range, 9-108). Results: Tumor DNA was extracted from 113 primary tumors in 122 patients. PIK3CA mutations were detected in 36 (32%) of the 113 tumors. Plasma samples were available from 34 (94%) of 36 patients with PIK3CA-mutated tumors. Among these 34 patients, the ctDNA patterns were as follows: 17 were persistent-negative, 14 were cleared, two were persistent-positive, and one was post-NAC-emergent. Post-surgical ctDNA was negative in all patients. pCR occurred in nine patients (26%), including five of 17 persistent-negative patients and four of 14 cleared patients, whereas none of the persistent-positive or post-NAC-emergent patients achieved pCR. Follow-up for distant recurrence was available for 33 patients. Distant metastasis developed in five patients: Three in the persistent-negative group, one in the cleared group, and one in the persistent-positive group. Although persistent-positive patients showed a numerically higher metastatic rate (one of two), most late distant relapses arose from preoperative ctDNA-negative patterns. Conclusions: In PIK3CA-mutated breast cancer treated with NAC, pre-surgical ctDNA positivity indicated residual disease but did not reliably predict long-term outcomes. A two-point ctDNA assessment may be insufficient for prognostic stratification. Further long-term follow-up and large-scale studies are needed to validate these findings. Citation Format: Ayaka Sato, Takayuki Ueno, Shunji Takahashi, Yoshinori Murakami, Masahiko Tanabe. Circulating tumor DNA dynamics predict the response to neoadjuvant chemotherapy but not long-term outcomes in PIK3CA-mutated breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 5323.